CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/01/16 18:13:54 | Available memory: 1.232 GB INPUT: Reading input from 'pt-criteria.in' [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [strip :WAT,Na+,Cl-] Warning: Action specified before trajin/ensemble. Assuming trajin. STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c3] Reading '../ctraj.c3' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*). Best-fit RMSD will be calculated, coords will be rotated and translated. [nativecontacts :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9', contacts set up based on first frame. Distance cutoff is 7 Angstroms, imaging is on. Mask selection will not include solvent. Data set name: Contacts_00002 Saving minimum observed distances in set 'Contacts_00002[mindist]' Contact stats will be written to 'STDOUT' Contact res pairs will be written to 'STDOUT' [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] VECTORMATH: Calculating Angle from dot product of vectors v_base1 and v_base2 Vectors will be normalized. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7174 of 7174) Coordinate processing will occur on 7174 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr' Warning: Setup incomplete for [strip]: Skipping 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](42) Reference mask: [:1,2&!@H*](42) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [nativecontacts :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 6: [vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c3 (1-7174, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 72 native contacts: Atom ':2@N9' to ':1@N9' Atom ':2@N9' to ':1@C8' Atom ':2@N9' to ':1@N7' Atom ':2@N9' to ':1@N3' Atom ':2@N9' to ':1@C4' Atom ':2@C8' to ':1@N9' Atom ':2@C8' to ':1@C8' Atom ':2@C8' to ':1@N7' Atom ':2@C8' to ':1@C5' Atom ':2@C8' to ':1@N3' Atom ':2@C8' to ':1@C4' Atom ':2@N7' to ':1@N9' Atom ':2@N7' to ':1@C8' Atom ':2@N7' to ':1@N7' Atom ':2@N7' to ':1@C5' Atom ':2@N7' to ':1@C6' Atom ':2@N7' to ':1@C2' Atom ':2@N7' to ':1@N3' Atom ':2@N7' to ':1@C4' Atom ':2@C5' to ':1@N9' Atom ':2@C5' to ':1@C8' Atom ':2@C5' to ':1@N7' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C4' Atom ':2@C6' to ':1@N9' Atom ':2@C6' to ':1@C8' Atom ':2@C6' to ':1@N7' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@O6' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C4' Atom ':2@N6' to ':1@N9' Atom ':2@N6' to ':1@C8' Atom ':2@N6' to ':1@N7' Atom ':2@N6' to ':1@C5' Atom ':2@N6' to ':1@C6' Atom ':2@N6' to ':1@O6' Atom ':2@N6' to ':1@N1' Atom ':2@N6' to ':1@C2' Atom ':2@N6' to ':1@N2' Atom ':2@N6' to ':1@N3' Atom ':2@N6' to ':1@C4' Atom ':2@N1' to ':1@N9' Atom ':2@N1' to ':1@C8' Atom ':2@N1' to ':1@N7' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@O6' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C4' Atom ':2@C2' to ':1@N9' Atom ':2@C2' to ':1@C8' Atom ':2@C2' to ':1@N7' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C4' Atom ':2@N3' to ':1@N9' Atom ':2@N3' to ':1@C8' Atom ':2@N3' to ':1@N7' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C4' Atom ':2@C4' to ':1@N9' Atom ':2@C4' to ':1@C8' Atom ':2@C4' to ':1@N7' Atom ':2@C4' to ':1@C5' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 7174 frames and processed 7174 frames. TIME: Avg. throughput= 61770.8091 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 44.0747 72 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N9 5941 0.828 4.89 0.725 2 :2@N7_:1@N9 5927 0.826 5.26 0.752 3 :2@C6_:1@N9 5880 0.82 4.52 0.788 4 :2@N6_:1@N9 5819 0.811 4.46 0.852 5 :2@C4_:1@N9 5782 0.806 5.36 0.62 6 :2@N1_:1@N9 5725 0.798 4.69 0.764 7 :2@C8_:1@N9 5678 0.791 5.83 0.624 8 :2@C6_:1@C8 5666 0.79 4.57 0.815 9 :2@N6_:1@C8 5654 0.788 4.28 0.962 10 :2@C6_:1@C4 5654 0.788 5.07 0.814 11 :2@C5_:1@C8 5611 0.782 5.09 0.731 12 :2@C2_:1@N9 5593 0.78 5.15 0.733 13 :2@N6_:1@C4 5578 0.778 4.89 0.9 14 :2@N1_:1@C8 5561 0.775 4.76 0.866 15 :2@N3_:1@N9 5553 0.774 5.53 0.654 16 :2@C5_:1@C4 5541 0.772 5.51 0.698 17 :2@N1_:1@C4 5524 0.77 5.16 0.787 18 :2@N9_:1@N9 5480 0.764 5.95 0.524 19 :2@N7_:1@C8 5447 0.759 5.43 0.861 20 :2@N6_:1@N7 5389 0.751 4.67 0.905 21 :2@C2_:1@C8 5329 0.743 5.36 0.872 22 :2@C6_:1@N3 5327 0.743 5.43 0.875 23 :2@C6_:1@N7 5303 0.739 5.13 0.745 24 :2@C4_:1@C8 5300 0.739 5.68 0.622 25 :2@N6_:1@C5 5294 0.738 5 0.905 26 :2@C5_:1@N3 5259 0.733 5.79 0.742 27 :2@C2_:1@C4 5250 0.732 5.63 0.706 28 :2@C6_:1@C5 5229 0.729 5.39 0.774 29 :2@N1_:1@N7 5224 0.728 5.25 0.822 30 :2@C4_:1@C4 5222 0.728 5.98 0.587 31 :2@N1_:1@N3 5195 0.724 5.48 0.851 32 :2@N6_:1@N3 5179 0.722 5.33 1.02 33 :2@N1_:1@C5 5155 0.719 5.47 0.801 34 :2@N7_:1@C4 5087 0.709 5.82 0.651 35 :2@N3_:1@C8 5012 0.699 5.83 0.751 36 :2@C5_:1@N7 4923 0.686 5.76 0.656 37 :2@C4_:1@N3 4907 0.684 6.13 0.582 38 :2@N3_:1@C4 4898 0.683 6.05 0.6 39 :2@N7_:1@N3 4668 0.651 6.03 0.731 40 :2@C5_:1@C5 4659 0.649 5.95 0.637 41 :2@C8_:1@C8 4586 0.639 6.04 0.709 42 :2@C2_:1@N7 4459 0.622 5.83 0.831 43 :2@C2_:1@C5 4285 0.597 5.97 0.732 44 :2@N6_:1@C6 4263 0.594 5.53 0.901 45 :2@N9_:1@C8 4258 0.594 6.23 0.549 46 :2@N7_:1@N7 4168 0.581 6.01 0.771 47 :2@C8_:1@C4 3984 0.555 6.32 0.496 48 :2@N6_:1@C2 3849 0.537 5.53 1.07 49 :2@C6_:1@C2 3848 0.536 5.82 0.869 50 :2@C6_:1@C6 3799 0.53 5.96 0.734 51 :2@N1_:1@C6 3767 0.525 5.96 0.769 52 :2@C4_:1@N7 3680 0.513 6.25 0.536 53 :2@N9_:1@C4 3646 0.508 6.45 0.459 54 :2@N7_:1@C5 3626 0.505 6.16 0.627 55 :2@N6_:1@N1 3423 0.477 5.61 0.97 56 :2@N6_:1@O6 3303 0.46 5.84 0.808 57 :2@C8_:1@N3 3217 0.448 6.27 0.561 58 :2@C4_:1@C5 3168 0.442 6.35 0.524 59 :2@N9_:1@N3 3109 0.433 6.4 0.502 60 :2@N3_:1@N7 3033 0.423 6.2 0.709 61 :2@C6_:1@N1 2954 0.412 5.98 0.779 62 :2@C5_:1@C2 2896 0.404 6.13 0.702 63 :2@N3_:1@C5 2800 0.39 6.34 0.627 64 :2@N6_:1@N2 2445 0.341 5.48 1.1 65 :2@N1_:1@O6 2162 0.301 6.19 0.74 66 :2@C6_:1@O6 2114 0.295 6.19 0.632 67 :2@N7_:1@C2 2072 0.289 6.13 0.658 68 :2@C5_:1@C6 2055 0.286 6.3 0.554 69 :2@C8_:1@N7 1765 0.246 6.27 0.655 70 :2@C8_:1@C5 1403 0.196 6.44 0.47 71 :2@N7_:1@C6 1369 0.191 6.39 0.481 72 :2@N9_:1@N7 1263 0.176 6.41 0.449 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 7174, 'v_base2' size 7174, output size 7174 TIME: Analyses took 0.0009 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 7174 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 7174 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 7174 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 7174 COM "COM" (double, distance), size is 7174 v_base1 "v_base1" (vector, vector), size is 7174 v_base2 "v_base2" (vector, vector), size is 7174 normalangle "normalangle" (double), size is 7174 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.02%) TIME: Trajectory Process : 0.1161 s ( 98.99%) TIME: Action Post : 0.0002 s ( 0.19%) TIME: Analysis : 0.0009 s ( 0.75%) TIME: Data File Write : 0.0000 s ( 0.02%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1173 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 0.1625 seconds. -------------------------------------------------------------------------------- To cite CPPTRAJ use: Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095.